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| 2. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
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| 5. |
- Chen, Jing-Ling, et al.
(author)
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Quantum contextuality for a relativistic spin-1/2 particle
- 2013
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In: Physical Review A. Atomic, Molecular, and Optical Physics. - 1050-2947 .- 1094-1622. ; 87:2, s. 022109-
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Journal article (peer-reviewed)abstract
- The quantum predictions for a single nonrelativistic spin-1/2 particle can be reproduced by noncontextual hidden variables. Here we show that quantum contextuality for a relativistic electron moving in a Coulomb potential naturally emerges if relativistic effects are taken into account. The contextuality can be identified through the violation of noncontextuality inequalities. We also discuss quantum contextuality for the free Dirac electron as well as the relativistic Dirac oscillator. DOI: 10.1103/PhysRevA.87.022109
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| 6. |
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| 7. |
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| 8. |
- Tang, Ting-Ting, et al.
(author)
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Impaired thymic export and apoptosis contribute to regulatory T-cell defects in patients with chronic heart failure.
- 2011
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203 .- 1932-6203. ; 6:9, s. e24272-
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Journal article (peer-reviewed)abstract
- Animal studies suggest that regulatory T (T(reg)) cells play a beneficial role in ventricular remodeling and our previous data have demonstrated defects of T(reg) cells in patients with chronic heart failure (CHF). However, the mechanisms behind T(reg-)cell defects remained unknown. We here sought to elucidate the mechanism of T(reg-)cell defects in CHF patients.
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| 9. |
- Wei, Tao, et al.
(author)
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Molecular and catalytic characterization of a phi class glutathione transferase from Cathaya argyrophylla
- 2012
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In: Biochemical Systematics and Ecology. - Oxford : Pergamon Press. - 0305-1978 .- 1873-2925. ; 40, s. 75-85
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Journal article (peer-reviewed)abstract
- Plant phi class glutathione transferases (GSTs) play important roles in stress tolerance and detoxification metabolism. This study reports the cloning, expression and biochemical characteristics of a phi GST gene (CaGSTF) from the endemic and endangered conifer Cathaya argyrophylla. The recombinant CaGSTF showed GSH-conjugating activity towards the substrate NED-Cl and CDNB. Kinetic analysis revealed low catalytic efficiency with a k(cat)/K-m(GSH) value of 9.82 mM(-1)S(-1). The CaGSTF proved to be a thermolabile enzyme, at 40 degrees C the enzyme's activity was nearly abolished. Site-directed mutagenesis revealed that Ser12, Lys42, Ile55, Glu67 and Ser68 of CaGSTF are critical components of glutathione-binding sites that contribute to the enzyme's catalytic activity. Compared to other plant phi GSTs and conifer tau GSTs, CaGSTF showed a narrow substrate spectrum, low catalytic efficiency and thermolability. These atypical properties suggest the enzyme may have a limited functional role in the organism's adaptation to environmental stresses in the subtropical regions. (C) 2011 Elsevier Ltd. All rights reserved.
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| 10. |
- Aad, G, et al.
(author)
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- 2015
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swepub:Mat__t
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